Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6914 to 6963 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
1729 Ranked autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 187.582 190.028 1.01304
Squared dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 13960 15382.4 1.10189
Rooted protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] 70.2384 72.4913 1.03208
1730 Measured phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] 6259.8 6684.3 1.06781
Ranked chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 215.336 212.567 1.01303
Squared structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] 18074.5 19915.8 1.10187
Rooted spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 70.2391 72.4922 1.03208
1731 Measured lamin b2. [swissprot;acc:q03252] 5840.77 6236.53 1.06776
Ranked aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] 215.336 212.567 1.01303
Squared sr rich protein. [refseq;acc:nm_032870] 35530.1 32245.4 1.10187
Rooted band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 70.2389 72.4919 1.03208
1732 Measured proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 5781.8 6173.1 1.06768
Ranked aarf domain containing kinase 4. [refseq;acc:nm_024876] 215.336 212.567 1.01303
Squared chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 18074.5 19915.8 1.10187
Rooted band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 70.2384 72.4914 1.03208
1733 Measured elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 5874.83 6272.26 1.06765
Ranked aarf domain containing kinase 1. [refseq;acc:nm_020421] 215.336 212.567 1.01303
Squared mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 28523.1 31428.2 1.10185
Rooted 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 70.2391 72.4922 1.03208
1734 Measured zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] 5874.83 6272.26 1.06765
Ranked nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] 221.921 219.081 1.01296
Squared hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 26278.9 28944.8 1.10145
Rooted band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 70.2384 72.4912 1.03207
1735 Measured elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] 5874.83 6272.26 1.06765
Ranked leucyl-trna synthetase. [refseq;acc:nm_020117] 218.99 216.189 1.01296
Squared exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] 26592.4 29289.7 1.10143
Rooted elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] 62.3876 64.3877 1.03206
1736 Measured twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 5925.65 6326.43 1.06763
Ranked transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] 221.921 219.081 1.01296
Squared phd finger protein 9. [refseq;acc:nm_018062] 26592.4 29289.7 1.10143
Rooted elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] 62.3692 64.3688 1.03206
1737 Measured rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] 5925.65 6326.43 1.06763
Ranked probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 218.99 216.189 1.01296
Squared small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] 26592.4 29289.7 1.10143
Rooted elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] 62.4076 64.4076 1.03205
1738 Measured ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 5885.08 6282.97 1.06761
Ranked lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] 206.595 209.258 1.01289
Squared homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 20110 18258 1.10143
Rooted porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 57.4522 59.2916 1.03202
1739 Measured argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] 5695.57 6079.61 1.06743
Ranked tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 206.595 209.258 1.01289
Squared homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 20103.6 18253.7 1.10134
Rooted galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 70.2226 72.4707 1.03201
1740 Measured serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] 5878.2 6274.27 1.06738
Ranked defender against cell death 1 (dad-1). [swissprot;acc:p46966] 206.595 209.258 1.01289
Squared ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 20093.8 18247 1.10121
Rooted methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] 64.9517 67.0286 1.03198
1741 Measured serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 6297.05 6721.08 1.06734
Ranked t-complex 11. [refseq;acc:nm_018679] 206.595 209.258 1.01289
Squared proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 29747.7 32753.1 1.10103

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/